Contact experts in Gromacs to get answers
2,926 views 1,562 posts
Questions related to Gromacs
Hi everyone, I need to buy a new laptop. I do the first steps of molecular dynamics by GROMACS (on Ubuntu) with my laptop, but I don't need to do equilibration or final MD run here, I do them on...
29 September 2020 9,808 4 View
I performed in-silico acetylation using PyTM plugin but there are certain clashes that I want to resolve. I couldn't perform energy minimization using gromacs, chimera as they do not have default...
27 September 2020 4,119 6 View
My system consists of ionic liquids, aliphatic and aromatic hydrocarbons. Any suggestions and any script for calculation of viscosity?
25 September 2020 6,795 1 View
I was trying to apply restraints on my molecules, however, they were still moving after I put 100000kJ/mol/nm^2 on them. I am sure my topology is correct, so I think maybe its the correlation of...
24 September 2020 4,353 3 View
I am using Ubuntu 20.04 and I have PyMol installed, with a license. But it has been impossible to add the repository ppa:makson96/dynamics. Even downloaded from github, the package with the...
21 September 2020 7,184 1 View
Hello everybody I use gromacs software but I do not know what code to use to get the number of water molecules in the carbon nanotube. If anyone can help Please Thanks a lot🙏
13 September 2020 1,228 6 View
Hello Everyone, I am using gromacs for MD simulation of the protein-ligand complex. I am using CHARMM force field but it is continuously showing the following error. I checked and some people...
10 September 2020 2,329 3 View
Dear all, I am looking for a way to restrain the center of mass (COM) of two different molecules bathed in water, using GROMACS 2018. The only thing close I found on gromacs that does this is the...
08 September 2020 5,115 8 View
Dear all, I have done simulation of two carbohydrate molecules in Gromacs with simulation box length of 6 nm. I have corrected the trajectory using trjconv with pbc mol and center flag as used in...
05 September 2020 531 5 View
Hello, I've used GROMACS to perform a short REMD simulation (200 ps) in order to test whether my choice of temperature range allowed sufficient exchanges between replicas. The REMD simulations...
03 September 2020 9,632 3 View
I'm using Gromacs 2020.3 for molecular dynamics calculations using an AMD Rx 580 GPU. However, analyzing the log files I realized that in fact the Intel GPU of the CPU itself is being used and not...
29 August 2020 3,838 1 View
Hi :D I'm using Gromacs 5.1.5 for MD simulation. For binding energy calculation, I used g_mmpbsa (version 5.1.2) I simulated the protein for 150ns and nojump of my xtc file. Then cut last 50ns for...
26 August 2020 7,840 1 View
Hi everyone, I am new gromacs user. I am doing the MD simulation of protein-NA. I did the Energy minimization step, NVT, NPT equilibration. after equilibrating the system i submitted the...
22 August 2020 8,169 4 View
I chose C-alpha as a group for root mean square calculation(rmsf), but why my rmsf calculation in gromacs did still count on atom-based, not residue-based? The command I used: gmx rmsf -f...
18 August 2020 1,584 6 View
Dear all, I want to distance restrain for an ion and its associated residue. There are 5 polymer chain and 200 ions( 40 for each chain). I made restrain.itp for my desire atoms and their...
11 August 2020 4,740 1 View
Dear researchers, I want to simulate a polymer at micro molar concentration in GROMACS. Whenever I try with simulation box of about 30 nm each side , the force is not converging. Therefore, if I...
02 August 2020 3,531 3 View
After obtaining EIS results, I have used an equivalent electrical circuit to fit the spectrum. It is comprised of Rs (CPE II Rct and W). Charge transfer resistance and Warburg impedance elements...
30 July 2020 6,493 2 View
I have performed MD simulation to a trans membrane protein using gromacs 2018. Can anyone provide me way to calculate the tilt angle of the protein relative to bilayer? Also how can I calculate...
17 July 2020 8,314 1 View
Dear Researchers, I am quite new at using Gromacs, and trying to add H to my .PDB file using Gromacs. Though i added H using Maestro in my PDB file, gromacs gives error like 'Atom XXX in resiude...
15 July 2020 1,593 3 View
Hello, I've made an octane slab and would like to place a protein in it using lambada. Usually I use a membrane and then place the protein in it, and lambada has always worked. Now, it gives me...
15 July 2020 9,190 0 View
I was recently running a long MD simulation using GROMACS 2020.2. The system unexpectedly approximately 1/2 of the way through due to a segmentation fault. I attempted a restart using teh...
14 July 2020 3,769 0 View
Dear researchers, please i used MD simulation for the complexe protein-ligand using gromacs software. but in equilibration phase i put this commands: gmx mdrun -deffnm nvt nsteps = 50000 and...
11 July 2020 2,840 0 View
Hi all, I'm trying to plot Free Energy Landscapes from Gromacs after using the gmx sham function. After using the command: gmx sham -f PCAplot2d.xvg -notime -ls gibbs1-2.xpm (where...
08 July 2020 1,441 1 View
It seems that polarization has been implemented in the Gromacs version of 2019 and further. However, I can't seem to find relevant info in the documentation except for the edits that have to be...
01 July 2020 2,141 3 View